The biocidal cations of Cu and Zn were hosted on the surfaces and in the cavities of X zeolite via ion exchange. The microstructure and interface properties of the exchanged zeolite X samples were analyzed by XRD, SEM, XPS, and XRF. The as-prepared samples showed excellent antimicrobial activity towards gram-negative bacteria of Escherichia coli and gram-positive bacteria of Staphylococcus aureus. Furthermore, the batch antimicrobial experiments showed that the bacterial disinfection process fitted well with the first order model. The Cu-zeolite showed excellent and better antibacterial performance on S. aureus than on E. coli, and the mortalities of E. coli and S. aureus were almost 100% after 1 h with the initial Cu-zeolite concentrations of 1000 ppm and 100 ppm, respectively. However, the Zn-zeolites were found to be less effective on S. aureus than on E. coli, and the mortalities of E. coli and S. aureus were almost 100% after 1 h with the initial Zn-zeolite concentrations of 500 ppm and 1000 ppm, respectively. In addition, the relationships between the apparent rate constant (k) and reagent concentration (C) were also systematically investigated. The present results suggest that the as-prepared samples could be promising antibacterial materials for the efficient disinfection of contaminated water with bacteria.